# gse129166 <- getGEO("GSE129166")
Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 2)
gse <- getGEO(filename="Data/GSE129166_series_matrix.txt.gz")
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpO2Degc/GPL570.soft.gz
gse
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 212 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM3701699 GSM3701700 ... GSM3701910 (212 total)
varLabels: title geo_accession ... tissue:ch1 (41 total)
varMetadata: labelDescription
featureData
featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 31378695
Annotation: GPL570
fData(gse)
pData(gse)
data.frame(exprs(gse))
#GSE34748
#gse34748 <- getGEO("GSE34748") # Then go to file loc and move downloaded file to data folder
Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 2)
gse <- getGEO(filename="Data/GSE34748_series_matrix.txt.gz")
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpO2Degc/GPL570.soft.gz
gse
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 56 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM854492 GSM854493 ... GSM854547 (56 total)
varLabels: title geo_accession ... tissue:ch1 (32 total)
varMetadata: labelDescription
featureData
featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 22335458
Annotation: GPL570
fData(gse)
pData(gse)
data.frame(exprs(gse))
getGEO("GSE51675")
Found 1 file(s)
GSE51675_series_matrix.txt.gz
$GSE51675_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 41093 features, 18 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM1250391 GSM1250392 ... GSM1250408 (18 total)
varLabels: title geo_accession ... treatment:ch1 (41 total)
varMetadata: labelDescription
featureData
featureNames: (+)E1A_r60_1 (+)E1A_r60_3 ... RC9 (41093 total)
fvarLabels: ID SPOT_ID ... SEQUENCE (17 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 25925804
Annotation: GPL6480
getGEO("GSE343")
Found 2 file(s)
GSE343-GPL271_series_matrix.txt.gz
GSE343-GPL272_series_matrix.txt.gz
$`GSE343-GPL271_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 28032 features, 66 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM4776 GSM4777 ... GSM4841 (66 total)
varLabels: title geo_accession ... data_row_count (43 total)
varMetadata: labelDescription
featureData
featureNames: 1 2 ... 28784 (28032 total)
fvarLabels: ID NAME ... SPOT_ID (21 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 12853585
Annotation: GPL271
$`GSE343-GPL272_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 37632 features, 1 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM4842
varLabels: title geo_accession ... data_row_count (43 total)
varMetadata: labelDescription
featureData
featureNames: 1 2 ... 37632 (37632 total)
fvarLabels: ID NAME ... LUID (20 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 12853585
Annotation: GPL272
getGEO("GSE15296")
Found 1 file(s)
GSE15296_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpO2Degc/GPL570.soft.gz
$GSE15296_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 75 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM382248 GSM382249 ... GSM382322 (75 total)
varLabels: title geo_accession ... tissue:ch1 (38 total)
varMetadata: labelDescription
featureData
featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 24725967
Annotation: GPL570
getGEO("GSE46474")
Found 1 file(s)
GSE46474_series_matrix.txt.gz
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpO2Degc/GPL570.soft.gz
$GSE46474_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54613 features, 40 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM1130812 GSM1130813 ... GSM1130851 (40 total)
varLabels: title geo_accession ... tissue:ch1 (46 total)
varMetadata: labelDescription
featureData
featureNames: 1007_s_at 1053_at ... 91952_at (54613 total)
fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 25387159
Annotation: GPL570
getGEO("GSE50084")
Found 1 file(s)
GSE50084_series_matrix.txt.gz
$GSE50084_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 29096 features, 115 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM1213867 GSM1213868 ... GSM1213981 (115 total)
varLabels: title geo_accession ... tissue:ch1 (32 total)
varMetadata: labelDescription
featureData
featureNames: 7896736 7896738 ... 8180418 (29096 total)
fvarLabels: ID GB_LIST ... category (12 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
pubMedIds: 26484130
Annotation: GPL6244